Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data |
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Authors: | Petr Novák Pavel Neumann Ji?í Macas |
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Institution: | (1) Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic |
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Abstract: | Background The investigation of plant genome structure and evolution requires comprehensive characterization of repetitive sequences
that make up the majority of higher plant nuclear DNA. Since genome-wide characterization of repetitive elements is complicated
by their high abundance and diversity, novel approaches based on massively-parallel sequencing are being adapted to facilitate
the analysis. It has recently been demonstrated that the low-pass genome sequencing provided by a single 454 sequencing reaction
is sufficient to capture information about all major repeat families, thus providing the opportunity for efficient repeat
investigation in a wide range of species. However, the development of appropriate data mining tools is required in order to
fully utilize this sequencing data for repeat characterization. |
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Keywords: | |
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